Harvard Catalyst Profiles

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Matthew Couger, Ph.D.


Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
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  1. Anderson N, Jaron KS, Hodson CN, Couger MB, Ševcík J, Weinstein B, Pirro S, Ross L, Roy SW. Gene-rich X chromosomes implicate intragenomic conflict in the evolution of bizarre genetic systems. Proc Natl Acad Sci U S A. 2022 06 07; 119(23):e2122580119. PMID: 35653559; PMCID: PMC9191650.
    Citations:    Fields:    Translation:AnimalsCells
  2. Couger MB, Roy SW, Anderson N, Gozashti L, Pirro S, Millward LS, Kim M, Kilburn D, Liu KJ, Wilson TM, Epps CW, Dizney L, Ruedas LA, Campbell P. Sex chromosome transformation and the origin of a male-specific X chromosome in the creeping vole. Science. 2021 05 07; 372(6542):592-600. PMID: 33958470.
    Citations: 2     Fields:    Translation:AnimalsCells
  3. Lakhey N, Sierra-Alvarez R, Couger MB, Krzmarzick MJ, Field JA. Anammox enrichment culture has unexpected capabilities to biotransform azole contaminants of emerging concern. Chemosphere. 2021 Feb; 264(Pt 2):128550. PMID: 33065321.
    Citations:    Fields:    
  4. Couger MB, Graham C, Fathepure BZ. Genome Sequence of Lignin-Degrading Arthrobacter sp. Strain RT-1, Isolated from Termite Gut and Rumen Fluid. Microbiol Resour Announc. 2020 Jan 16; 9(3). PMID: 31948970; PMCID: PMC6965588.
    Citations: 1     
  5. Wang Y, Youssef NH, Couger MB, Hanafy RA, Elshahed MS, Stajich JE. Molecular Dating of the Emergence of Anaerobic Rumen Fungi and the Impact of Laterally Acquired Genes. mSystems. 2019 Aug 27; 4(4). PMID: 31455637; PMCID: PMC6712302.
    Citations: 7     
  6. Murphy CL, Youssef NH, Hanafy RA, Couger MB, Stajich JE, Wang Y, Baker K, Dagar SS, Griffith GW, Farag IF, Callaghan TM, Elshahed MS. Horizontal Gene Transfer as an Indispensable Driver for Evolution of Neocallimastigomycota into a Distinct Gut-Dwelling Fungal Lineage. Appl Environ Microbiol. 2019 08 01; 85(15). PMID: 31126947; PMCID: PMC6643240.
    Citations: 23     Fields:    Translation:Animals
  7. Ayalew S, Confer AW, Couger MB. Genome Sequence of a Bovine Isolate of Pasteurella multocida Strain 232. Microbiol Resour Announc. 2019 May 16; 8(20). PMID: 31097504; PMCID: PMC6522789.
  8. Lim A, Naidenov B, Bates H, Willyerd K, Snider T, Couger MB, Chen C, Ramachandran A. Nanopore ultra-long read sequencing technology for antimicrobial resistance detection in Mannheimia haemolytica. J Microbiol Methods. 2019 04; 159:138-147. PMID: 30849421.
    Citations: 10     Fields:    Translation:AnimalsCells
  9. Couger MB, Arévalo L, Campbell P. A High Quality Genome for Mus spicilegus, a Close Relative of House Mice with Unique Social and Ecological Adaptations. G3 (Bethesda). 2018 07 02; 8(7):2145-2152. PMID: 29794166; PMCID: PMC6027863.
    Citations: 2     Fields:    Translation:AnimalsCells
  10. Calkins SS, Elledge NC, Mueller KE, Marek SM, Couger MB, Elshahed MS, Youssef NH. Development of an RNA interference (RNAi) gene knockdown protocol in the anaerobic gut fungus Pecoramyces ruminantium strain C1A. PeerJ. 2018; 6:e4276. PMID: 29404209; PMCID: PMC5796279.
    Citations: 4     
  11. Ayalew S, Confer AW, Hansen RD, Couger MB. Genome Sequence of Mannheimia haemolytica Serotype 1 Strain 16041065 BH. Genome Announc. 2017 Apr 06; 5(14). PMID: 28385859; PMCID: PMC5383907.
  12. Ayalew S, Confer AW, Hansen RD, Couger MB. Genome Sequence of a Spontaneous Nonhemolytic Mutant of Mannheimia haemolytica 16041065 GH. Genome Announc. 2017 Apr 06; 5(14). PMID: 28385858; PMCID: PMC5383906.
  13. Jackson CA, Couger MB, Prabhakaran M, Ramachandriya KD, Canaan P, Fathepure BZ. Isolation and characterization of Rhizobium sp. strain YS-1r that degrades lignin in plant biomass. J Appl Microbiol. 2017 Apr; 122(4):940-952. PMID: 28092137.
    Citations: 10     Fields:    Translation:AnimalsCells
  14. Bryant DM, Johnson K, DiTommaso T, Tickle T, Couger MB, Payzin-Dogru D, Lee TJ, Leigh ND, Kuo TH, Davis FG, Bateman J, Bryant S, Guzikowski AR, Tsai SL, Coyne S, Ye WW, Freeman RM, Peshkin L, Tabin CJ, Regev A, Haas BJ, Whited JL. A Tissue-Mapped Axolotl De Novo Transcriptome Enables Identification of Limb Regeneration Factors. Cell Rep. 2017 01 17; 18(3):762-776. PMID: 28099853; PMCID: PMC5419050.
    Citations: 247     Fields:    Translation:AnimalsCells
  15. Calkins S, Couger MB, Jackson C, Zandler J, Hudgins GC, Hanafy RA, Budd C, French DP, Hoff WD, Youssef N. Draft genome sequence of Staphylococcus hominis strain Hudgins isolated from human skin implicates metabolic versatility and several virulence determinants. Genom Data. 2016 Dec; 10:91-96. PMID: 27766204; PMCID: PMC5065635.
  16. Moghadam F, Couger MB, Russ B, Ramsey R, Hanafy RA, Budd C, French DP, Hoff WD, Youssef N. Draft genome sequence and detailed analysis of Pantoea eucrina strain Russ and implication for opportunistic pathogenesis. Genom Data. 2016 Dec; 10:63-68. PMID: 27699151; PMCID: PMC5037212.
    Citations: 2     
  17. Avramov AP, Couger MB, Hartley EL, Land C, Wellendorf R, Hanafy RA, Budd C, French DP, Hoff WD, Youssef N. Draft genome sequence of Microbacterium oleivorans strain Wellendorf implicates heterotrophic versatility and bioremediation potential. Genom Data. 2016 Dec; 10:54-60. PMID: 27699150; PMCID: PMC5035333.
    Citations: 3     
  18. Hanafy RA, Couger MB, Baker K, Murphy C, O'Kane SD, Budd C, French DP, Hoff WD, Youssef N. Draft genome sequence of Micrococcus luteus strain O'Kane implicates metabolic versatility and the potential to degrade polyhydroxybutyrates. Genom Data. 2016 Sep; 9:148-53. PMID: 27583205; PMCID: PMC4993860.
    Citations: 3     
  19. Miller NT, Fuller D, Couger MB, Bagazinski M, Boyne P, Devor RC, Hanafy RA, Budd C, French DP, Hoff WD, Youssef N. Draft genome sequence of Pseudomonas moraviensis strain Devor implicates metabolic versatility and bioremediation potential. Genom Data. 2016 Sep; 9:154-9. PMID: 27583206; PMCID: PMC4993851.
    Citations: 4     
  20. Schneider WDH, Gonçalves TA, Uchima CA, Couger MB, Prade R, Squina FM, Dillon AJP, Camassola M. Penicillium echinulatum secretome analysis reveals the fungi potential for degradation of lignocellulosic biomass. Biotechnol Biofuels. 2016; 9:66. PMID: 26989443; PMCID: PMC4794826.
    Citations: 13     
  21. Couger MB, Wright A, Lutter EI, Youssef N. Draft Genome Sequences of Five Pseudomonas aeruginosa Clinical Strains Isolated from Sputum Samples from Cystic Fibrosis Patients. Genome Announc. 2016 Jan 28; 4(1). PMID: 26823574; PMCID: PMC4732327.
  22. Couger MB, Hanafy RA, Edens C, Budd C, French DP, Hoff WD, Elshahed MS, Youssef NH. Draft Genome of the Arthrobacter sp. Strain Edens01. Genome Announc. 2015 Dec 17; 3(6). PMID: 26679586; PMCID: PMC4683231.
  23. Couger MB, Hanafy RA, Mitacek RM, Budd C, French DP, Hoff WD, Elshahed MS, Youssef NH. The Draft Genome Sequence of Xanthomonas sp. Strain Mitacek01 Expands the Pangenome of a Genus of Plant Pathogens. Genome Announc. 2015 Dec 10; 3(6). PMID: 26659686; PMCID: PMC4675951.
  24. Couger MB, Youssef NH, Struchtemeyer CG, Liggenstoffer AS, Elshahed MS. Transcriptomic analysis of lignocellulosic biomass degradation by the anaerobic fungal isolate Orpinomyces sp. strain C1A. Biotechnol Biofuels. 2015; 8:208. PMID: 26649073; PMCID: PMC4672494.
    Citations: 25     
  25. Al-Rubaye AA, Couger MB, Ojha S, Pummill JF, Koon JA, Wideman RF, Rhoads DD. Genome Analysis of Staphylococcus agnetis, an Agent of Lameness in Broiler Chickens. PLoS One. 2015; 10(11):e0143336. PMID: 26606420.
    Citations: 16     Fields:    Translation:AnimalsCells
  26. Frahm KA, Peffer ME, Zhang JY, Luthra S, Chakka AB, Couger MB, Chandran UR, Monaghan AP, DeFranco DB. Research Resource: The Dexamethasone Transcriptome in Hypothalamic Embryonic Neural Stem Cells. Mol Endocrinol. 2016 Jan; 30(1):144-54. PMID: 26606517; PMCID: PMC4695633.
    Citations: 11     Fields:    Translation:AnimalsCells
  27. Couger MB, Hurlbut A, Murphy CL, Budd C, French DP, Hoff WD, Elshahed MS, Youssef NH. Draft Genome Sequence of the Environmental Isolate Chryseobacterium sp. Hurlbut01. Genome Announc. 2015 Sep 17; 3(5). PMID: 26383650; PMCID: PMC4574379.
    Citations: 6     
  28. Mandelli F, Oliveira Ramires B, Couger MB, Paixão DA, Camilo CM, Polikarpov I, Prade R, Riaño-Pachón DM, Squina FM. Draft Genome Sequence of the Thermophile Thermus filiformis ATCC 43280, Producer of Carotenoid-(Di)glucoside-Branched Fatty Acid (Di)esters and Source of Hyperthermostable Enzymes of Biotechnological Interest. Genome Announc. 2015 May 14; 3(3). PMID: 25977443; PMCID: PMC4432349.
    Citations: 1     
  29. Prabhakaran M, Couger MB, Jackson CA, Weirick T, Fathepure BZ. Genome Sequences of the Lignin-Degrading Pseudomonas sp. Strain YS-1p and Rhizobium sp. Strain YS-1r Isolated from Decaying Wood. Genome Announc. 2015 Mar 05; 3(2). PMID: 25744986; PMCID: PMC4358373.
    Citations: 4     
  30. Struchtemeyer CG, Ranganathan A, Couger MB, Liggenstoffer AS, Youssef NH, Elshahed MS. Survival of the anaerobic fungus Orpinomyces sp. strain C1A after prolonged air exposure. Sci Rep. 2014 Nov 04; 4:6892. PMID: 25367149.
    Citations: 1     Fields:    Translation:AnimalsCells
  31. Youssef NH, Couger MB, McCully AL, Criado AE, Elshahed MS. Assessing the global phylum level diversity within the bacterial domain: A review. J Adv Res. 2015 May; 6(3):269-82. PMID: 26257925; PMCID: PMC4522544.
    Citations: 22     Fields:    
  32. Couger MB, Pipes L, Squina F, Prade R, Siepel A, Palermo R, Katze MG, Mason CE, Blood PD. Enabling large-scale next-generation sequence assembly with Blacklight. Concurr Comput. 2014 Sep 10; 26(13):2157-2166. PMID: 25294974.
    Citations: 2     
  33. Haas BJ, Papanicolaou A, Yassour M, Grabherr M, Blood PD, Bowden J, Couger MB, Eccles D, Li B, Lieber M, MacManes MD, Ott M, Orvis J, Pochet N, Strozzi F, Weeks N, Westerman R, William T, Dewey CN, Henschel R, LeDuc RD, Friedman N, Regev A. De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis. Nat Protoc. 2013 Aug; 8(8):1494-512. PMID: 23845962.
    Citations: 2860     Fields:    Translation:AnimalsCells
  34. Youssef NH, Couger MB, Struchtemeyer CG, Liggenstoffer AS, Prade RA, Najar FZ, Atiyeh HK, Wilkins MR, Elshahed MS. The genome of the anaerobic fungus Orpinomyces sp. strain C1A reveals the unique evolutionary history of a remarkable plant biomass degrader. Appl Environ Microbiol. 2013 Aug; 79(15):4620-34. PMID: 23709508.
    Citations: 72     Fields:    Translation:AnimalsCells
  35. Youssef NH, Couger MB, Elshahed MS. Fine-scale bacterial beta diversity within a complex ecosystem (Zodletone Spring, OK, USA): the role of the rare biosphere. PLoS One. 2010 Aug 26; 5(8):e12414. PMID: 20865128.
    Citations: 34     Fields:    Translation:Cells
  36. Liggenstoffer AS, Youssef NH, Couger MB, Elshahed MS. Phylogenetic diversity and community structure of anaerobic gut fungi (phylum Neocallimastigomycota) in ruminant and non-ruminant herbivores. ISME J. 2010 Oct; 4(10):1225-35. PMID: 20410935.
    Citations: 64     Fields:    Translation:AnimalsCells
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Funded by the NIH National Center for Advancing Translational Sciences through its Clinical and Translational Science Awards Program, grant number UL1TR002541.